My strategy for Gentoo, more or less:
/etc/ - all modified configuration files, including
/etc/portage/ - make.conf, package configuration (package.accept_keywords, package.use, and friends)
/var/lib/portage/ - world, and world sets. basically everything portage needs to rebuild the system
/var/db/repos/ - notably local and/or self-owned package repos
/home/<username>/ - no explanation needed
/root/ - no explanation needed
This should contain enough to pretty much rebuild a Gentoo system from a clean downloadable Stage onwards without (too much) intervention.
/etc/ - all modified configuration files, including
/etc/portage/ - make.conf, package configuration (package.accept_keywords, package.use, and friends)
/var/lib/portage/ - world, and world sets. basically everything portage needs to rebuild the system
/var/db/repos/ - notably local and/or self-owned package repos
/home/<username>/ - no explanation needed
/root/ - no explanation needed
This should contain enough to pretty much rebuild a Gentoo system from a clean downloadable Stage onwards without (too much) intervention.